I agree with you that he was in a depleted physical state to absorb sage chakra, but I thought sage mode helps the user recover faster from physical damage and lessen pain? I can't really get the exact fatcs now but here's what i found
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Is the recovery here different from healing? I remember the sage toad mentioning something about this during naruto's training at mount myoboku, and for some reason (which i think is sage mode), naruto was able to recover and withstand the kyubi rampage against pain since he was shown in sage mode immediately after the rampage.